/zotero-notes

/zotero-notes - Zotero to Obsidian Reading Notes

Read papers from the Zotero collection "$collection" and create or update detailed reading notes.

Default target

• Preferred target: the bound Obsidian project knowledge base (Sources/Papers/*.md)
• Fallback target: reading-notes-{collection}.md in the working directory if the current repo is not bound to Obsidian

Workflow

Step 0: Resolve whether the current repo is Obsidian-bound

1. If .claude/project-memory/registry.yaml exists for the current repo, treat the bound vault as the primary output target.
2. If the repo is a research project but not yet bound, bootstrap it first.
3. If there is no bound project context, fall back to a plain markdown output in the working directory.
4. Treat this command as an explicit agent-first ingestion pass under $zotero-obsidian-bridge.

Step 1: Load papers from Zotero

1. Call mcp__zotero__zotero_get_collections to find the matching collection.
2. Call mcp__zotero__zotero_get_collection_items to list the papers.
3. For each item, call:
   • mcp__zotero__zotero_get_item_metadata
   • mcp__zotero__zotero_get_item_fulltext when a PDF is available
   • mcp__zotero__zotero_get_annotations when helpful
   • mcp__zotero__zotero_get_notes when helpful
4. If MCP transport fails but a local zotero-mcp checkout is available, use the local Python fallback instead of stopping the pass.
5. Treat Zotero webpage items as weak-source inputs unless they clearly expose full paper metadata and useful full text. Abstract-only or placeholder pages must stay To-Read and cannot support Knowledge or Writing claims.

Step 2: Create/update the canonical paper note

If the project is Obsidian-bound, create or update one canonical note per paper under Sources/Papers/.

Each detailed note should contain:

• Claim
• Research question
• Method
• Evidence
• Strengths
• Limitation
• Direct relevance to repo
• Relation to other papers
• Knowledge links
• Optional downstream hooks
• canonical Evidence Record with Source type and Claim strength when the paper has reusable claims

Recommended frontmatter fields:

• title, authors, year, venue, doi, url, citekey, zotero_key
• keywords, concepts, methods
• related_papers, linked_knowledge, argument_claims, argument_methods, argument_gaps, paper_relationships

Prefer updating the existing note over creating a sibling note.

Step 3: Collection coverage and synthesis

After the paper-note pass:

• update a collection inventory note when the source is a named collection
• record item -> canonical note mapping and coverage counts such as 16 / 16
• verify coverage against expected Zotero keys, DOI values, or arXiv IDs when the user supplied them
• label abstract-only and webpage-placeholder items separately in the inventory
• synthesize durable literature knowledge under Knowledge/, for example:
  • Knowledge/Literature Overview.md
  • Knowledge/Method Taxonomy.md
  • Knowledge/Research Gaps.md

Prefer updating existing canonical knowledge notes over creating parallel summaries.

Step 4: Refresh the default literature canvas

After batch note creation or substantial note updates, refresh:

python3 "${CLAUDE_PLUGIN_ROOT}/skills/obsidian-literature-workflow/scripts/build_literature_canvas.py" --cwd "$PWD"

This rebuilds Maps/literature.canvas from paper-note and knowledge-note links.

Step 5: Optional synthesis outputs

• If format=comparison and promoted claims pass the evidence gate, also update Writing/comparison-matrix.md.
• If the paper batch already supports a thematic synthesis and promoted claims pass the evidence gate, update Writing/related-work-draft.md. If not, write only a coverage warning or claim map.

Step 6: Minimal write-back

Always update:

• today's Daily/YYYY-MM-DD.md
• repo-local binding summary when project state changes

Step 7: Final response

Include:

• collection size and coverage summary
• created / updated note paths
• optional obsidian://open links
• optional obsidian open ... suggestions when CLI is available

Fallback behavior

If the repo is not bound to Obsidian:

• create reading-notes-{collection}.md
• if format=comparison and promoted claims pass the evidence gate, also create comparison-matrix.md

Notes

• Zotero remains the source of truth for collection structure, metadata, attachments, PDF full text, and annotations.
• Obsidian remains the durable project knowledge surface for reading notes, project relevance, and cross-note linking.
• Default bridge targets are Sources/Papers/ and Knowledge/.
• Do not dump raw full text into Obsidian paper notes.
• Do not create Concepts/ or Datasets/ trees by default.
• Refresh Maps/literature.canvas by default after a substantial Zotero ingestion pass.
• Treat Experiments/ and Results/ as later project workflows, not the default Zotero-import destination.
• Do not let abstract-only or webpage-placeholder items support durable claims.